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The poke in the eye given to prime minister David Cameron by Tory rebels who want a referendum on Europe is causing turmoil in Whitehall. For a start, it has underlined a degree of confusion in Number 10 over who is responsible for what when it comes to advising the PM. There are concerns among diplomats that the PM, William Hague, foreign secretary, and chancellor George Osborne are sending rather different signals to other European leaders.

Worst of all is the nightmare prospect of the PM trying to negotiate the repatriation of powers to the UK from Europe without any bargaining counters. Talk about sending a leader naked into the conference chamber – and with Angela Merkel waiting to pounce.

The row over Europe will not have been helped by what I’m told is a muddled set-up at Number 10. No one seems certain who’s in charge of what except that the hand of Steve Hilton, the PM’s shoeless policy guru, seems to be felt everywhere. Word is that there are various side spats going on, with reports that Mr Hilton and strategy director Andrew Cooper have an uneasy relationship. More worrying is that the lines of advice reaching the PM from the Foreign Office, the National Security Council and the cabinet office are not always dovetailing. There are even reports – unconfirmed – that the PM “jumped the gun” on Libya and sent in the planes without consulting the NSC, though Sir Peter Ricketts, outgoing national security adviser, may have been personally asked for advice.

Whatever the problems in Number 10, Monday’s rebellion by eurosceptic Tory MPs came as a shock to officials who believed the issue of a referendum on Europe had been safely “parked” until after 2015. “Whitehall assumed that the PM meant it when he said this wasn’t a matter for this parliament,” says one diplomatic knight. “His argument was that the Lib Dems in the coalition wouldn’t allow a referendum.” This week Foreign Office officials have been dusting down the plans they drew up before the general election for hammering out a deal with other European leaders on bringing back powers to the UK – but it will not be easy.

“The big problem,” confided my knight, “is that Whitehall knows our bargaining position is extremely weak. Germany’s Angela Merkel is saying the 17 members of the eurozone could sign a new treaty of their own, ignoring the other members of the union. We’d have nothing to ratify – no excuse for a referendum. When Merkel put that to Cameron, he had no reply. Even if all 27 EU members were negotiating a new treaty, the fact is that we don’t have anything they want.”

I am assured that Sir Jon Cunliffe, the PM’s hugely respected adviser on foreign affairs, will have thought of this – but few will have expected such problems now. And there are worries the PM will have annoyed the Europeans by “barracking them from the side of field”. Mr Hague’s talk of the eurozone being like a burning building with no exit will have upset them even more. Mr Osborne, say insiders, seems to have a better understanding of the problems facing his fellow finance ministers and has been less strident. With the Tory rebels triumphant, it is becoming a truly wicked issue for the PM. On top of which, I’m told he may have to hang around for hours in Brussels today waiting for a decision from the eurozone 17.

In the bag

The Europe rebellion was triggered by a petition to the Commons signed by more than 100,000 people. Petitioning parliament goes back a long way – the first was submitted in 1327. There is still a large green bag on the back of the Speaker’s chair in which paper petitions are placed – hence the expression “it’s in the bag”. The e-petition on Europe is dwarfed by some in the past.

The Chartist petition of 1842, calling for electoral reform, had 3.5m signatures. Another one, drawn up in 1890, backing local taxation was eight and half miles long. Most petitions make little impact but the government has decreed that those with more than 100,000 signatures should go to the Commons backbench business committee, which under the latest reforms may allocate time for a debate and a vote. The committee does not have to call a debate – which may be fortunate.

Says one senior backbencher: “We could have a petition to bring back hanging. And drawing and quartering. In public. Sharia law would have nothing on us.”